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Mutant hydroxyphenylpyruvate dioxygenase polypeptides and methods of use
8269068 Mutant hydroxyphenylpyruvate dioxygenase polypeptides and methods of use
Patent Drawings:Drawing: 8269068-10    Drawing: 8269068-11    Drawing: 8269068-12    Drawing: 8269068-2    Drawing: 8269068-3    Drawing: 8269068-4    Drawing: 8269068-5    Drawing: 8269068-6    Drawing: 8269068-7    Drawing: 8269068-8    
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Inventor: Hawkes, et al.
Date Issued: September 18, 2012
Application: 12/692,552
Filed: January 22, 2010
Inventors: Hawkes; Timothy Robert (Bracknell, GB)
Langford; Michael Phillip (Bracknell, GB)
Viner; Russell Colin (Bracknell, GB)
Vernooij; Bernardus Theodorus Maria (Research Triangle, NC)
Dale; Richard (Bracknell, GB)
Assignee: Syngenta Participations AG (Basel, CH)
Primary Examiner: Kruse; David H
Assistant Examiner:
Attorney Or Agent: Edwards; S. Matthew
U.S. Class: 800/300; 435/320.1; 536/23.2; 800/278; 800/298
Field Of Search:
International Class: A01H 5/00; C12N 15/29; C12N 15/82
U.S Patent Documents:
Foreign Patent Documents: WO 97/49816; WO 98/04685; WO 98/20144; WO 99/04021; WO 00/32757; WO 02/46387; WO 2008/150473; WO 2009/144079
Other References: Iris M. Fritze et al, "The Crystal Structures of Zea mays and Arabidopsis 4-Hydroxyphenylpyruvate Dioxygenase" Plant Physiol. vol. 134, p.1388-1400; Apr. 2004. cited by other.
International Search Report dated Aug. 30, 2010 , issued in corresponding International Application No. PCT/US2010/021879. cited by other.









Abstract: Compositions and methods for conferring hydroxyphenyl pyruvate dioxygenase (HPPD) herbicide resistance or tolerance to plants are provided. Compositions include amino acid sequences, and variants and fragments thereof, for mutant HPPD polypeptides. Nucleic acids that encode the mutant HPPD polypeptides are also provided. Methods for conferring herbicide resistance or tolerance, particularly resistance or tolerance to certain classes of herbicides that inhibit HPPD, in plants are further provided. Methods are also provided for selectively controlling weeds in a field at a crop locus and for the assay, characterization, identification and selection of the mutant HPPDs of the current invention that provide herbicide tolerance.
Claim: That which is claimed:

1. A polynucleotide encoding a polypeptide having at least 80% sequence identity to SEQ ID NO:27, wherein said polypeptide has HPPD enzymatic activity and comprises theamino acid sequence G(I,V) LVD(R,K)D (SEQ ID NO:30), wherein L is replaced with any other amino acid.

2. The polynucleotide according to claim 1 selected from the group consisting of: a) a polynucleotide comprising the sequence set forth in SEQ ID NO:11; b) a polynucleotide having at least 85% sequence identity to the sequence set forth in SEQID NO: 11; c) a polynucleotide encoding the amino acid sequence set forth in SEQ ID NO: 24; d) a polynucleotide encoding the amino acid sequence of a polypeptide having at least 80% sequence identity the amino acid sequence set forth in SEQ ID NO: 24,wherein said polypeptide has HPPD enzymatic activity.

3. The polynucleotide of claim 1, wherein the nucleotide sequence is optimized for expression in a plant.

4. An expression cassette comprising the polynucleotide of claim 1 operably linked to a promoter that drives expression in a plant or plant cell.

5. The expression cassette of claim 4 further comprising an operably linked polynucleotide sequence encoding a polypeptide that confers a desirable trait.

6. The expression cassette of claim 5, wherein said desirable trait is resistance or tolerance to an herbicide.

7. The expression cassette of claim 6, wherein said desirable trait is resistance or tolerance to an HPPD inhibitor, glyphosate, or glufosinate.

8. The expression cassette of claim 7, wherein said polypeptide that confers a desirable trait is a cytochrome P450 or variant thereof.

9. The expression cassette of claim 8, wherein said polypeptide that confers a desirable trait is an EPSPS (5-enol-pyrovyl-shikimate-3-phosphate-synthase).

10. The expression cassette of claim 8, wherein said polypeptide that confers a desirable trait is a phosphinothricin acetyl transferase.

11. A vector comprising an expression cassette according to claim 4.

12. The vector of claim 11, wherein said vector comprises a polynucleotide comprising the sequence set forth in SEQ ID NO:33, 34, 35, or 36.

13. A method for conferring resistance or tolerance to an HPPD inhibitor in a plant, said method comprising introducing into said plant at least one expression cassette according to claim 4.

14. A transformed plant cell comprising at least one expression cassette according to claim 4.

15. The plant cell of claim 14, wherein said plant cell is a rice, barley, potato, sweet potato, canola, sunflower, rye, oats, wheat, corn, soybean, sugar beet, tobacco, Miscanthus grass, Switch grass, safflower, trees, cotton, cassava, tomato,sorghum, alfalfa, sugar beet, and sugarcane plant cell.

16. The plant cell of claim 15, wherein said plant cell is a soybean plant cell.

17. A plant, plant part, or seed comprising the plant cell of claim 14.

18. A method of controlling weeds at a locus, said method comprising applying to said locus a weed-controlling amount of one or more HPPD inhibitors, wherein said locus comprises a plant according to claim 17.

19. The method of claim 18, wherein said HPPD inhibitor is selected from the group consisting of: a) a compound of formula (Ia) ##STR00023## wherein R.sup.1 and R.sup.2 are hydrogen or together form an ethylene bridge; R.sup.3 is hydroxy orphenylthio-; R.sup.4 is halogen, nitro, C.sub.1-C.sub.4alkyl, C.sub.1-C.sub.4alkoxy-C.sub.1-C.sub.4alkyl-, C.sub.1-C.sub.4alkoxy-C.sub.1-C.sub.4alkoxy-C.sub.1-C.sub.4alkyl-; X is methine, nitrogen, or C--R.sup.5 wherein R.sup.5 is hydrogen,C.sub.1-C.sub.4alkoxy, C.sub.1-C.sub.4haloalkoxy-C.sub.1-C.sub.4alkyl-, or a group ##STR00024## and R.sup.6 is C.sub.1-C.sub.4alkylsulfonyl- or C.sub.1-C.sub.4haloalkyl; b) a compound of formula (Ib) ##STR00025## R.sup.1 and R.sup.2 are independentlyC.sub.1-C.sub.4alkyl; and the free acids thereof; c) a compound of formula (Ic) ##STR00026## wherein R.sup.1 is hydroxy, phenylcarbonyl-C.sub.1-C.sub.4alkoxy- or phenylcarbonyl-C.sub.1-C.sub.4alkoxy- wherein the phenyl moiety is substituted inpara-position by halogen or C.sub.1-C.sub.4alkyl, or phenylsulfonyloxy- or phenylsulfonyloxy- wherein the phenyl moiety is substituted in para-position by halogen or C.sub.1-C.sub.4alkyl; R.sup.2 is C.sub.1-C.sub.4alkyl; R.sup.3 is hydrogen orC.sub.1-C.sub.4alkyl; R.sup.4 and R.sup.6 are independently halogen, C.sub.1-C.sub.4alkyl, C.sub.1-C.sub.4haloalkyl, or C.sub.1-C.sub.4alkylsulfonyl-; and R.sup.5 is hydrogen, C.sub.1-C.sub.4alkyl, C.sub.1-C.sub.4alkoxy-C.sub.1-C.sub.4alkoxy-, or agroup ##STR00027## d) a compound of formula (Id) ##STR00028## wherein R.sup.1 is hydroxy; R.sup.2 is C.sub.1-C.sub.4alkyl; R.sup.3 is hydrogen; and R.sup.4, R.sup.5 and R.sup.6 are independently C.sub.1-C.sub.4alkyl; e) a compound of formula (Ie)##STR00029## wherein R.sup.1 is cyclopropyl; R.sup.2 and R.sup.4 are independently halogen, C.sub.1-C.sub.4haloalkyl, or C.sub.1-C.sub.4alkylsulfonyl-; and R.sup.3 is hydrogen; f) a compound of formula (If) ##STR00030## wherein R.sup.1 is cyclopropyl; R.sup.2 and R.sup.4 are independently halogen, C.sub.1-C.sub.4haloalkyl, or C.sub.1-C.sub.4alkylsulfonyl-; and R.sup.3 is hydrogen; and g) a compound of formula (Ig) or Formula (Ih) ##STR00031## wherein:-- R.sup.2 is selected from the group consistingof C.sub.1-C.sub.3alkyl, C.sub.1-C.sub.3haloalkyl, C.sub.1-C.sub.3alkoxy-C.sub.1-C.sub.3 alkyl and C.sub.1-C.sub.3alkoxy-C.sub.2-C.sub.3alkoxy-C.sub.1-C.sub.3-alkyl; R.sup.5 is hydrogen or methyl; R.sup.6 is selected from the group consisting ofhydrogen, fluorine, chlorine, hydroxyl and methyl; R.sup.7 is selected from the group consisting of hydrogen, halogen, hydroxyl, sulfhydryl, C.sub.1-C.sub.6alkyl, C.sub.3-C.sub.6cycloalkyl, C.sub.1-C.sub.6haloalkyl, C.sub.2-C.sub.6haloalkenyl,C.sub.2-C.sub.6alkenyl, C.sub.3-C.sub.6alkynyl, C.sub.1-C.sub.6alkoxy, C.sub.4-C.sub.7 cycloalkoxy, C.sub.1-C.sub.6haloalkoxy, C.sub.1-C.sub.6alkylthio, C.sub.1-C.sub.6alkylsulfinyl, C.sub.1-C.sub.6alkylsulfonyl, C.sub.1-C.sub.6haloalkylthio, amino,C.sub.1-C.sub.6alkylamino, C.sub.2-C.sub.6dialkylamino, C.sub.2-C.sub.6dialkylaminosulfonyl, C.sub.1-C.sub.6alkylaminosulfonyl, C.sub.1-C.sub.6alkoxy-C.sub.1-C.sub.6alkyl, C.sub.1-C.sub.6alkoxy-C.sub.2-C.sub.6alkoxy,C.sub.1-C.sub.6alkoxy-C.sub.2-C.sub.6alkoxy-C.sub.1-C.sub.6-alkyl, C.sub.3-C.sub.6alkenyl-C.sub.2-C.sub.6alkoxy, C.sub.3-C.sub.6alkynyl-C.sub.1-C.sub.6alkoxy, C.sub.1-C.sub.6alkoxycarbonyl, C.sub.1-C.sub.6alkylcarbonyl, C.sub.1-C.sub.4alkylenyl-S(O)p-R',C.sub.1-C.sub.4alkyleneyl-CO.sub.2--R', C.sub.1-C.sub.4alkyleneyl-(CO)N--R'R', phenyl, phenylthio, phenylsulfinyl, phenylsulfonyl, phenoxy, pyrrolidinyl, piperidinyl, morpholinyl and 5 or 6-membered heteroaryl or heteroaryloxy, the heteroaryl containingone to three heteroatoms, each independently selected from the group consisting of oxygen, nitrogen and sulphur, wherein the phenyl or heteroaryl component may be optionally substituted by a substituent selected from the group consisting ofC.sub.1-C.sub.3alkyl, C.sub.1-C.sub.3haloalkyl, C.sub.1-C.sub.3 alkoxy, C.sub.1-C.sub.3haloalkoxy, halo, cyano, and nitro; X=O or S; n=0 or 1; m=0 or 1 with the proviso that if m=1 then n=0 and if n=1 then m=0; p=0, 1, or 2; R' is independentlyselected from the group consisting of hydrogen and C.sub.1-C.sub.6alkyl; R.sup.8 is selected from the group consisting of hydrogen, C.sub.1-C.sub.6alkyl, C.sub.1-C.sub.6haloalkyl, C.sub.1-C.sub.6alkylcarbonyl-C.sub.1-C.sub.3alkyl,C.sub.3-C.sub.6cycloalkylalkeneyl for example cyclohexylmethylenyl, C.sub.3-C.sub.6alkynylalkyleneyl for example propargyl, C.sub.2-C.sub.6-alkenylalkylenyl for example allyl, C.sub.1-C.sub.6alkoxy C.sub.1-C.sub.6alkyl, cyano-C.sub.1-C.sub.6-alkyl,arylcarbonyl-C.sub.1-C.sub.3-alkyl (wherein the aryl may be optionally substituted with a substituent selected from the group consisting of halo, C.sub.1-C.sub.3-alkoxy, C.sub.1-C.sub.3-alkyl, C.sub.1-C.sub.3 haloalkyl), aryl-C.sub.1-C.sub.6alkyl(wherein the aryl may be optionally substituted with a substituent selected from the group consisting of halo, C.sub.1-C.sub.3-alkoxy, C.sub.1-C.sub.3-alkyl, C.sub.1-C.sub.3 haloalkyl), C.sub.1-C.sub.6alkoxy C.sub.1-C.sub.6alkoxy C.sub.1-C.sub.6alkyl anda 5 or 6-membered heteroaryl-C.sub.1-C.sub.3-alkyl or heterocyclyl-C.sub.1-C.sub.3-alkyl, the heteroaryl or heterocyclyl containing one to three heteroatoms, each independently selected from the group consisting of oxygen, nitrogen and sulphur, whereinthe heterocyclyl or heteroaryl component may be optionally substituted by a substituent selected from the group consisting of halo, C.sub.1-C.sub.3alkyl, C.sub.1-C.sub.3haloalkyl, and C.sub.1-C.sub.3 alkoxy; Q is selected from the group consisting of:##STR00032## wherein A.sup.1 is selected from the group consisting of O, C(O), S, SO, SO.sub.2 and (CR.sup.eR.sup.f).sub.q; q=0, 1 or 2; R.sup.a, R.sup.b, R.sup.c, R.sup.d, R.sup.e and R.sup.f are each independently selected from the group consistingof C.sub.1-C.sub.4alkyl which may be mono-, di- or tri-substituted by substituents selected from the group consisting of C.sub.1-C.sub.4alkoxy, halogen, hydroxy, cyano, hydroxycarbonyl, C.sub.1-C.sub.4alkoxycarbonyl, C.sub.1-C.sub.4alkylthio,C.sub.1-C.sub.4alkylsulfinyl, C.sub.1-C.sub.4alkylsulfonyl, C.sub.1-C.sub.4alkylcarbonyl, phenyl and heteroaryl, it being possible for the phenyl and heteroaryl groups in turn to be mono-, di- or tri-substituted by substituents selected from the groupconsisting of C.sub.1-C.sub.4alkoxy, halogen, hydroxy, cyano, hydroxycarbonyl, C.sub.1-C.sub.4alkoxycarbonyl, C.sub.1-C.sub.4alkylsulfonyl and C.sub.1-C.sub.4haloalkyl, the substituents on the nitrogen in the heterocyclic ring being other than halogen; or R.sup.a, R.sup.b, R.sup.c, R.sup.d, R.sup.e and R.sup.f are each independently selected from the group consisting of hydrogen, C.sub.1-C.sub.4alkoxy, halogen, hydroxy, cyano, hydroxycarbonyl, C.sub.1-C.sub.4alkoxycarbonyl, C.sub.1-C.sub.4alkylthio,C.sub.1-C.sub.4alkylsulfinyl, C.sub.1-C.sub.4alkylsulfonyl, C.sub.1-C.sub.4alkylcarbonyl, phenyl or heteroaryl, it being possible for the phenyl and heteroaryl groups in turn to be mono-, di- or tri-substituted by substituents selected from the groupconsisting of C.sub.1-C.sub.4alkoxy, halogen, hydroxy, cyano, hydroxycarbonyl, C.sub.1-C.sub.4alkoxycarbonyl, C.sub.1-C.sub.4alkylsulfonyl and C.sub.1-C.sub.4haloalkyl, the substituents on the nitrogen in the heterocyclic ring being other than halogen; or R.sup.a and R.sup.b together form a 3- to 5-membered carbocyclic ring which may be substituted by C.sub.1-C.sub.4alkyl and may be interrupted by oxygen, sulfur, S(O), SO.sub.2, OC(O), NR.sup.g or by C(O); or R.sup.a and R.sup.c together form aC.sub.1-C.sub.3alkylene chain which may be interrupted by oxygen, sulfur, SO, SO.sub.2, OC(O), NR.sup.h or by C(O); it being possible for that C.sub.1-C.sub.3alkylene chain in turn to be substituted by C.sub.1-C.sub.4alkyl; R.sup.g and R.sup.h are eachindependently of the other C.sub.1-C.sub.4alkyl, C.sub.1-C.sub.4haloalkyl, C.sub.1-C.sub.4alkylsulfonyl, C.sub.1-C.sub.4alkylcarbonyl or C.sub.1-C.sub.4alkoxycarbonyl; R.sup.i is C.sub.1-C.sub.4alkyl; R.sup.3 is selected from the group consisting ofC.sub.1-C.sub.6alkyl, optionally substituted with halogen and/or C.sub.1-C.sub.3alkoxy; and C.sub.3-C.sub.6 cycloalkyl optionally substituted with halogen and/or C.sub.1-C.sub.3alkoxy; R.sup.9 is selected from the group consisting of cyclopropyl,CF.sub.3 and i.-Pr; R.sup.10 is selected from the group consisting of hydrogen, I, Br, SR.sup.11, S(O)R.sup.11, S(O).sub.2R.sup.11 and CO.sub.2R.sup.11; and R.sup.11 is C.sub.1-4 alkyl.

20. The method of claim 19, wherein said HPPD inhibitor is mesotrione.

21. The polynucleotide of claim 1, wherein the L is replaced with M in the encoded polypeptide.

22. The polynucleotide of claim 1, wherein the L is replaced with A in the encoded polypeptide.
Description:
 
 
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